(1) Field of the Invention
The present invention generally relates to enzyme inhibitors and methods of discovering them. More particularly, the invention is directed to protein kinase inhibitors and methods using combinatorial libraries for identifying protein kinase inhibitors.
(2) Description of the Related Art
References Cited    Borowski, P.; Resch, K.; Schmitz, H.; Heiland, M.; Biol. Chem. 2000, 381, 19-27.    Chan, P. M.; Miller, W. T. Methods Mol. Biol. 1998, 84, 75-86.    Charp, P. A.; Rice, W. G.; Raynor, R. L.; Reimund, E.; Kinkade Jr., J. M.; Ganz, T.; Selsted, M. E.; Leher, R. I.; Kuo, R. F.; Biochem. Pharmacol. 1988, 37, 951-6.    Cortese, R.; Monaci, P.; Nicosia, A.; Luzzago, A.; Felici, F.; Galfre, G.; Pessi, A.; Tramontano, A.; Sollazzo, M. Curr. Opin. Biotechnol. 1995, 6, 73-80.    Djafarzadeh, S., and Niggli, V. Exp Cell Res 1997, 236, 427-435.    Dostmann, W. R.; Tegge, W.; Frank, R.; Nickl, C. K.; Taylor, M. S.; Brayden, J. E. Pharmacol. Ther. 2002, 93, 203-15.    Eichholtz, T.; de Bont, D. B. A.; de Widt, J.; Liskamp, R. M. J.; Ploegh, H. L.; J. Biol. Chem. 1993, 268, 1982-6.    Feng, S.; Kapoor, T. M.; Shirai, F.; Combs, A. P.; Schreiber, S. L.; Chem. Biol. 1996, 3, 661-70.    Ghosh, M., Ichetovkin, I., Song, X., Condeelis, J. S., and Lawrence, D. S. J Am Chem Soc 2002, 124, 2440-2441.    Ghosh, M., Song, X., Mouneimne, G., Sidani, M., Lawrence, D. S., and Condeelis, J. S. Science 2004, 304, 743-746.    Gschwendt, M., Muller, H. J., Kielbassa, K., Zang, R., Kittstein, W., Rincke, G., and Marks, F. Biochem Biophys Res Commun 2004, 199, 93-98.    Hofmann, J.; FASEB J. 1997, 11, 649-69.    House, C.; Kemp, B. E.; Science 1987, 238, 1726-8.    House, C., and Kemp, B. E.; Cell Signal 1990, 2, 187-190.    Ishii, H., Jirousek, M. R., Koya, D., Takagi, C., Xia, P., Clermont, A., Bursell, S. E., Kern, T. S., Ballas, L. M., Heath, W. F., Stramm, L. E., Feener, E. P., and King, G. L. Science 1996, 272, 728-731.    Jirousek, M. R., Gillig, J. R., Gonzalez, C. M., Heath, W. F., McDonald, J. H., 3rd, Neel, D. A., Rito, C. J., Singh, U., Stramm, L. E., Melikian-Badalian, A., Baevsky, M., Ballas, L. M., Hall, S. E., Winneroski, L. L., and Faul, M. M. J Med Chem 1996, 39, 2664-2671.    Kemp, B. E., Pearson, R. B., and House, C. M. Methods Enzymol 1991, 201, 287-304    Kuroda, S., Tokunaga, C., Kiyohara, Y., Higuchi, O., Konishi, H., Mizuno, K., Gill, G. N., and Kikkawa, U. J Biol Chem 1996, 271, 31029-31032.    Inagaki K. et al.; Circulation 2004, 108, 2304-7.    Lahn, M. et al.; Eur. J. Cancer 2004, 40, 10-20.    Lahn, M. M. et al.; Oncol. Rep. 2004, 11, 515-22.    Lahn, M. M., and Sundell, K. L. Melanoma Res 2004, 14, 85-89.    Lam, K. S.; Liu, R.; Miyamoto, S.; Lehman, A. L.; Tuscano, J. M. Acct. Chem. Res. 2003, 36, 370-7.    Lawrence, D. S.; Niu, J. Pharmacol. Ther. 1998, 77, 81-114.    Laudanna, C., Mochly-Rosen, D., Liron, T., Constantin, G., and Butcher, E. C. J Biol Chem 1998, 273, 30306-30315.    Laudanna, C., Sorio, C., Tecchio, C., Butcher, E. C., Bonora, A., Bassi, C., and Scarpa, A. Lab Invest 2003, 83, 1155-1163.    Lee, T. R.; Lawrence, D. S.; J. Med. Chem. 1999, 42, 784-7.    Lee, T. R., and Lawrence, D. S. J Med Chem 2000, 43, 1173-1179.    Lee, J. H., Nandy, S. K., and Lawrence, D. S. J Am Chem Soc 2004, 126, 3394-3395.    Liu, W. S., and Heckman, C. A. Cell Signal 1998, 10, 529-542.    Mackay, H. J., and Twelves, C. J. Endocr Relat Cancer 2003, 10, 389-396.    Martiny-Baron, G., Kazanietz, M. G., Mischak, H., Blumberg, P. M., Kochs, G., Hug, H., Marme, D., and Schachtele, C. J Biol Chem 1993, 268, 9194-9197.    Mochly-Rosen, D., and Kauvar, L. M. Semin Immunol 2001, 12, 55-61.    Nishikawa, K., Toker, A., Johannes, F. J., Songyang, Z., and Cantley, L. C. J Biol Chem 1997, 272, 952-960.    Munger, J.; Roizman, B.; Proc. Natl. Acad. Sci. USA 2001, 98, 10410-5.    Musashi, M; Ota, S; Shiroshita, N. Int. J. Hematol. 2000, 72, 12-19.    Nachman et al., 1995. Regul. Pept. 1995, 57, 359-370.    Nakashima, S.; J. Biochem. (Tokyo) 2002, 132, 669-75.    Neid, M. et al.; J. Biol. Chem. 2003 (e-published—PMID 14604996).    Nguyen, J. T.; Porter, M.; Amoui, M.; Miller, W. T.; Zuckermann, R. N.; Lim, W. A.; Chem. Biol. 2000, 7, 463-73.    Nishikawa, K.; Toker, A.; Johannes, F.-J.; Songyang, Z.; Cantley, L. C. J. Biol. Chem. 1997, 272, 952-60.    O'Brian, C. A.; Ward, N. E. Mol. Pharmacol. 1989, 36, 355-9.    Ricouart, A.; Tartar, A.; Sergheraert, C.; Biochem. Biophys. Res. Commun. 1989, 165, 1382-90.    Ron, D., Luo, J., and Mochly-Rosen, D. J Biol Chem 1995, 270, 24180-24187.    Sarin, V. K., Kent, S. B., Tam, J. P., and Merrifield, R. B. Anal Biochem 1981, 117, 147-157.    Selbie, L. A., Schmitz-Peiffer, C., Sheng, Y., and Biden, T. J. J Biol Chem 1993, 268, 24296-2430.    Shen, K.; Keng, Y.-F.; Wu, L.; Guo, X.-L.; Lawrence, D. S.; Zhang, Z.-Y. J. Biol. Chem. 2001, 276, 47311-19.    Sun, J. P., Fedorov, A. A., Lee, S. Y., Guo, X. L., Shen, K., Lawrence, D. S., Almo, S. C., and Zhang, Z. Y. J Biol Chem 2003, 278, 12406-12414.    Toker, A. Front Biosci 1998, 3, D1134-1147.    Tuttle, K. R., and Anderson, P. W. Am J Kidney Dis 2003, 42, 456-465.    Vetrie, D. et al.; Nature 1993, 361, 226-33.    Wang, Q. et al.; J. Biol. Chem. 2003, 278, 51091-9.    Ward, N. E.; Gravitt, K. R.; O'Brian, C. A.; Cancer Lett. 1995, 88, 37-40.    Way, K. J.; Chou, E.; King, G. L. Trends Pharmacol Sci, 2000, 21, 181-7.    Wilkinson, S. E., Parker, P. J., and Nixon, J. S. Biochem J 1993, 294 (Pt 2), 335-337.    Xie, L., Lee, S. Y., Andersen, J. N., Waters, S., Shen, K., Guo, X. L., Moller, N. P., Olefsky, J. M., Lawrence, D. S., and Zhang, Z. Y. Biochemistry 2003, 42, 12792-12804.    Yeh, R. H.; Lee, T. R.; Lawrence, D. S.; Pharmacol. Ther. 2002, 93, 179-91.    Yeh, R.-H., Lee, T. R. Lawrence, D. S. J. Biol. Chem. 2001, 276, 12235-40.    Zebda, N., Bernard, O., Bailly, M., Welti, S., Lawrence, D. S., and Condeelis, J. S. J Cell Biol 2000, 151, 1119-1128.    Zhan, Q., Bamburg, J. R., and Badwey, J. A. Cell Motil Cytoskeleton 2003, 54, 1-15.    U.S. Pat. No. 6,214,852.    U.S. Pat. No. 6,248,559.    U.S. Pat. No. 6,376,747.    U.S. Pat. No. 6,660,731.
Signal transduction is the biochemical mechanism by which information is transmitted between distinct cellular sites. Signaling pathways differ from their classical biochemical counterparts in a number of ways. For example, the enzymes of glycolysis and the TCA cycle catalyze the conversion of small molecules into products, which are then passed onto the next enzymatic member of the pathway. By contrast, the protein participants of signaling pathways primarily associate with and act upon one another.
An important group of eukaryotic and viral enzymes involved in these signaling pathways are protein kinases. Protein kinases are enzymes that transfer a phosphate group from a donor molecule, usually ATP, to an amino acid residue of a protein. In signal transduction, this protein phosphorylation can activate or inhibit the activity of the protein. Types of protein kinases include serine/threonine-specific protein kinases such as phosphorylase kinase, protein kinase A, protein kinase C, Ca2+/calmodulin-dependent protein kinase, MAP kinase, and Mos/Raf kinase; tyrosine-specific protein kinases such as receptor tyrosine kinase; histidine-specific protein kinases; and aspartic acid/glutamic acid-specific protein kinases.
Several deleterious conditions (including diseases) are associated with expression of protein kinases. These deleterious conditions include various cancers, various cardiovascular diseases, type 2 diabetes, agammaglobulinaemia, reperfusion injury, Alzheimer's disease, various neurological and neurodegenerative diseases, chemotherapy-induced alopecia, arthritis, various autoimmune diseases, various inflammatory diseases, allergies, asthma and viral virulence (Inagaki et al., 2003; Wang et al., 2003; Lahn et al., 2003, 2004; Neid et al. 2003; Vetrie et al., 1993; Stenberg et al., 2000; Munger and Roizman, 2001; U.S. Pat. Nos. 6,248,559; 6,214,852; 6,660,731).
Protein kinase C (PKC) is a family of protein kinases that generally require Ca2+, diacylglycerol (DAG) and a phospholipids such as phosphatidylcholine for activation. There are at least 11 isoforms (=isozymes) of mammalian PKC-α, βI, βII, γ, δ, ε, ζ, η, θ, τ/λ, and μ which vary by tissue distribution, activators and substrates.
PKCs are further classified as classical or conventional PKC (α, βI, βII, and γ), which require phospholipid, DAG or phorbol ester, and Ca2+ or activation; novel PKC (δ, ε, μ and θ), requiring phospholipid, DAG or phorbol ester, but not Ca2+, and atypical PKC (ζ and τ/λ), requiring phospholipid, but not DAG, phorbol ester, or Ca2+. Structural differences also distinguish these three groups of PKC from each other.
PKCs are known to be involved in many cellular functions, including cell proliferation, tumor promotion, differentiation, and apoptotic cell death. For a review of PKC structure and function, see Musashi et al., 2000.
The amino acid sequences (“consensus recognition sequences”) that drive critical protein-protein kinase interactions are readily identified using combinatorial peptide-based libraries (Lam et al., 2003; Cortese et al., 1995; Dostmann et al., 2002; Chan et al., 1998). Consensus sequence information has proven helpful in piecing together signaling pathways. In addition, peptides containing these sequences are potentially useful inhibitory reagents that could furnish information about the biological role of signaling proteins. Unfortunately, consensus sequence peptides tend to display modest affinities (KD or Ki>low μM) for their protein targets. We (Yeh et al., 2002; Yeh et al., 2001; Shen et al., 2001; Lee et al., 1999), as well as others (See, e.g., Nguyen et al., 2000; Feng et al., 1996), have shown that consensus sequences for signaling proteins can be converted into higher affinity ligands using the 3-dimensional structure of the protein target as a guide. Nevertheless, the tertiary structure for only a small minority of all signaling proteins has been assigned, thereby limiting the generality of this approach. There is thus a need for procedures for identification of inhibitors of protein kinases. The present invention addresses that need.